title: H3K4me3 histone ChIPseq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil dysfunction in HIV-infected individuals

status: Public on Mar 23 2021

city: Lodz

first: Przemyslaw

last: Lewkowicz

address: Pomorska 251/A4

department: Department of Neurology, Laboratory of Neuroimmunology

country: Poland

institute: Medical University of Lodz, Poland,

summary: In this study, we demonstrated dysregulation of DNA transcription in H3K4me3 histone in circulating neutrophils of HIV-infected subjects.  Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis revealed that the most spectacular abnormalities were observed in the exons, introns and promoter-TSS regions. Bioinformatic analysis of Gene Ontology, including biological processes, molecular function and cellular components, demonstrated that the main changes were related to the genes responsible for cell activation, cytokine production, adhesive molecule expression, histone remodeling via upregulation of methyltransferase process and downregulation of NF-kB transcription factor in canonical pathways. Abnormalities within H3K4me3 implicated LPS-mediated NF-kB canonical activation pathway that was a result of low amounts of kB DNA sites within histone H3K4me3, low NF-kB (p65 RelA) and TLR4 mRNA expression as well as reduced free NF-kB (p65 RelA) accumulation in the nucleus. ‘Panoramic view of the landscape gene’ within histone H3K4me3 led us postulate that impairment within the canonical NF-kB cell activation pathway may be the primary phenomenon responsible for neutrophil dysfunction observed in HIV-infected individuals

overall_design: Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis in circulating neutrophils isolated from HIV infected individuals compare to healthy volunteers


title: Remodeling of Mouse Hippocampus Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus

status: Public on Mar 24 2021

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

country: USA

institute: Prairie View A&M University

summary: TNF-like weak inducer of apoptosis (TWEAK) and its cognate receptor Fn14 have been shown to play an important role in neurocognitive dysfunction in murine lupus. We profiled and compared gene expression in the hippocampi of MRL/+, MRL/lpr and MRL/lpr-Fn14 knockout (Fn14ko) adult female mice to determine the transcriptomic impact of TWEAK/Fn14 on hippocampal gene expression in lupus. We found that the TWEAK/Fn14 pathway strongly affects the expression level, variability and coordination of the genomic fabrics responsible for neurotransmission and chemokine signaling. Dysregulation of the PI3K-Akt pathway in the MRL/lpr lupus strain compared with the MRL/+ control and Fn14ko mice was particularly prominent and therefore promising as a potential therapeutic target, although the complexity of the transcriptomic fabric highlights important considerations in in vivo experimental models.

overall_design:
Comparison of gene expression profiles in hippocampi of MRL/lpr, Fn14ko and MRL/MpJ adult female mice

Please note that [1] multiple yellow strategy was used to hybridize differently labelleld biological replicas with the microarray and then iteratively normalizing the expression data to the intra-array and inter-array median expression until the maximum error of estimate becomes less than 5% [2] Each raw data file contains raw data for two samples as indicated in the corresponding sample description field.

middle: A

first: Jing

last: Wen

first: Sanda

first: Noa

last: Schwartz

first: Chaim

last: Putterman


title: Affymetrix OncoScan SNP data for T-cell lymphoblastic lymphoma

status: Public on Mar 15 2021

city: Rochester

first: Xinjie

last: Xu

state: MN

address: 200 2nd St SW

institute: Mayo Clinic

summary:
We performed single nucleotide polymorphism (SNP) array profiling on 9 early T-cell precursor lymphoblastic lymphoma and 15 non-early T-cell precursor lymphoblastic lymphoma cases.
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from unstained slides.

overall_design: Analysis of copy number and copy-neutral loss-of-heterozygosity were performed using Affymetrix OncoScan SNP array on 9 early T-cell precursor lymphoblastic lymphoma (ETP-LLy) and 15 non-early T-cell precursor lymphoblastic lymphoma cases to study the genomic profile of ETP-LLy.

first: Rodney

middle: R

last: Miles


title: RNA-Seq data for dorsal root ganglia of RECTAS-treated ELP1/IKBKAP (IVS20+6T>C) transgenic mice

status: Public on Mar 10 2021

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

type: Expression profiling by high throughput sequencing

summary: ELP1/IKBKAP IVS20+6T>C is a causal mutation of familial disautonomia. Small molecule compound RECTAS efficiently suppress Exon 20 skipping, caused by this mutation. Its efficacy in vivo was evaluated by RNA-Seq for dorsal root ganglia from HsELP1 (IVS20+6T>C) transgenic mice, following p.o. administration of 0.5% carboxy methyl cellulose (CMC) or RECTAS (300 mg/kgBW).

overall_design: ELP1/IKBKAP (IVS20+6T>C) transgenic mice were p.o. administered for 0.5% carboxy methyl cellulose (CMC) or RECTAS (300 mg/kgBW), followed by second administration of the same dose 4 hours after the administration. Four hours after the second administration, mice were euthanized and RNA was extracted from dorsal root ganglia. Extracted RNAs were applied for RNA-Seq.

first: Masahiko

last: Ajiro

last: Iida

first: YoungJin

last: Kim

first: Adrian

last: Krainer

first: Masatoshi

last: Hagiwara


title: Adipose tissue myeloid cell RNAseq

city: Singapore

first: Christiane

last: Ruedl

state: Singapore

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Three different macrophage subsets and one subpopulation of monocyte derived cells were sorted from lean and obese mice adipose tissue

overall_design: 3 MHCIIlow macrophage subsets from lean and obese mice, 3 MHCII+CD11c- macrophage subsets from lean and obese mice, 3 MHCII+CD11c+ macrophage subsets from obese mice, and 3 monocyte derived cell subsets from lean and obese mice were compared

first: Qi

last: Chen


title: Overexpression of constitutively active Ikkb and/or loss of Stat3 in murine esophageal epithelium

status: Public on Apr 01 2021

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

summary: Many esophageal diseases arise in the context of chronic inflammation, but the role that esophageal epithelial cells play in initiating inflammation remains poorly understood. Since the IKKβ/NF-κB and STAT3 pathways are critical signaling hubs that drive inflammatory-mediated responses, we aimed to identify how these two pathways regulate gene expression in esophageal epithelial cells. In this study, we performed RNA-Seq analysis on esophageal epithelium from mice with overexpression of constitutively active Ikkb and/or loss of Stat3 specifically in esophageal epithelial cells.

overall_design: Cre recombinase specific to esophageal epithelial cells (EBV ED/L2-Cre) was used to drive gene expression. We compared gene expression between control mice (ROSA26-STOPf/f-Ikk2ca; Stat3 f/f), mice with conditional overexpression of constitutively active IKKβ (ED/L2-Cre; ROSA26-STOPf/f-Ikk2ca), mice with conditional STAT3 knockout (ED/L2-Cre; Stat3 f/f), and mice with both conditional overexpression of active IKKβ and STAT3 knockout (ED/L2-Cre; ROSA26-STOPf/f-Ikk2ca; Stat3 f/f). Esophagi were harvested at 6 weeks of age for gene expression analysis.

first: Kelsey

middle: N

last: Wiles


title: Next Generation Sequencing of wild type N2 and pan-neuronal overexpression of α-syn C. elegans fed with K12 BW25113 and csgA(-) bacteria

status: Public on Mar 20 2021

city: HK

first: Chaogu

last: Zheng

address: The University of Hong Kong, Pokfulam Road

department: School of Biological Science

country: Hong Kong

institute: University of Hong Kong

summary: The goal of this study is to extract differentially expressed genes between K12 BW25113 and csgA(-) fed N2 and PD C. elegans. Methods: mRNA profile of K12 BW25113 and csgA(-) fed N2 and UM10 strains were generated by deep sequencing in duplicates, using BGISEQ-500. Around 20 million reads were obtained for each sample and the reads were aligned to the C. elegans genome (WS235) using STAR 2.7. To identify genes differentially expressed, the transcript counts were analyzed using DESeq2, and genes with false discovery rate–corrected p values (q values) below 0.05 and fold change above 2 or below 0.5 were identified. qRT–PCR validation was performed using TB Green Premix Ex Taq kit.

overall_design: Transcriptome profile of N2 and PD model of C. elegans UM10 fed with K12 BW25113 and csgA(-) bacteria at L4 stage.

first: Chenyin

last: Wang

first: Chun

middle: Y

last: Lau

first: Fuqiang

last: Ma


title: Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage

status: Public on Mar 09 2021

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: Long noncoding RNAs (lncRNAs) have been shown to play important roles in gene regulatory networks acting in early development. There has been rapid turnover of lncRNA loci during vertebrate evolution, with few human lncRNAs conserved beyond mammals. The sequences of these rare deeply conserved lncRNAs are typically not similar to each other. Here, we characterize HOXA-AS3 and HOXB-AS3, lncRNAs produced from the central regions of the HOXA and HOXB clusters. Sequence-similar orthologs of both lncRNAs are found in multiple vertebrate species and there is evident sequence similarity between their promoters, suggesting that the production of these lncRNAs predates the duplication of the HOX clusters at the root of the vertebrate lineage. This conservation extends to similar expression patterns of the two lncRNAs, in particular in cells transiently arising during early development or in the adult colon. Functionally, the RNA products of HOXA-AS3 and HOXB-AS3 regulate the expression of their overlapping HOX5–7 genes both in HT-29 cells and during differentiation of human embryonic stem cells. Beyond production of paralogous protein-coding and microRNA genes, the regulatory program in the HOX clusters therefore also relies on paralogous lncRNAs acting in restricted spatial and temporal windows of embryonic development and cell differentiation.

overall_design: RNA-seq of HT-29 cells treated with siNT, siHOXA-AS3 and siHOXB-AS3

first: I

first: Y

last: Lubelsky


title: Hormone-responsive Bmpr1a maintains myoepithelial integrity during pregnancy

status: Public on Mar 05 2021

city: beijing

first: chunlei

last: shao

address: yuanmingyuan west road

country: China

institute: china agricultural university

summary: Myoepithelial and luminal cells synergistically expand in the mammary gland during pregnancy, and this process is precisely governed by hormone-related signaling pathways. The BMP signaling pathway is now known to play crucial roles in all organ systems. However, the functions of BMP signaling in the mammary gland remain unclear. Here, we found that Bmpr1a is upregulated by hormone-induced Sp1 at pregnancy. Using a doxycycline (Dox)-inducible Bmpr1a conditional knockout mouse model, we demonstrated that loss of Bmpr1a results in compromised myoepithelial integrity, reduced mammary stem cells and precocious alveolar differentiation during pregnancy. Mechanistically, Bmpr1a regulates the expression of p63 and Slug, two key regulators of myoepithelial maintenance, through pSmad1/5-Smad4 complexes, and consequently activate P-cadherin during pregnancy. Collectively, these findings identify a novel role of BMP signaling in maintaining the identity of myoepithelial cells and suppressing precocious alveolar formation.

overall_design: mammary epithelium of control and Bmpr1a cKO at pregnancy day 14.5

first: Chunlei

last: Shao


title: RNA-sequencing data of intestinal tissue of mice adminstered proanthocyanidins (PAC)

status: Public on Mar 04 2021

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We show here the transcriptional response in the distal small intestine of mice gavaged with two different PAC fractions

overall_design: RNA was obtained from the tissue of 5 mice gavaged with water, 5 mice gavaged with low molecular weight PAC, and 5 mice with 5 molecular weight PAC


title: Genes affected by L-arabinose in Salmonella Typhimurium biofilms

status: Public on Mar 31 2021

city: Columbus

first: John

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

summary: Genes were differentially expressed in wild-type Salmonella Typhimurium biofilms and an ΔaraE mutant when grown in the presence of 5mM or 40mM L-arabinose. Multiple biological pathways were impacted, including genes involved in arabinose metabolism, curli fimbriae, pentose phosphae pathway, TCA cycle. amino acid synthesis, pyrimidine and purine biosynthesis, and ATP synthesis.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Wild-type and ΔaraE mutant strains were grown in biofilm forming conditions in 96-well plates in M9 + 5mM or 40mM L-arabinose for 4 days. Cells were washed and harvested for RNA extraction for subsequent RNA-seq analsis.

first: Erin

middle: M

last: Vasicek

middle: S

first: James

last: Fitch

first: Peter

last: White


title: Elucidation of the BMI1 interactome identifies novel regulatory roles in glioblastoma

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

summary: Glioblastoma (GBM) is the most common and aggressive intrinsic brain tumour in adults. Epigenetic mechanisms controlling normal brain development are often dysregulated in GBM. Among these, BMI1, a structural component of the Polycomb Repressive Complex 1 (PRC1), which promotes the H2AK119ub catalytic activity of Ring1B, is upregulated in GBM and its tumorigenic role has been shown in vitro and in vivo. Here, we have used protein and chromatin immunoprecipitation followed by mass spectrometry (MS) analysis to elucidate the protein composition of PRC1 in GBM and CRISPR/dCAS9-mediated modulation of BMI1 to assess its influence on protein interactions. We show that while well-established BMI1 functions such as control of cell proliferation and cell adhesion are PRC1-dependent, novel regulatory functions in mRNA splicing and cholesterol transport are PRC1 independent and may represent novel targetable mechanisms in GBM.

overall_design: Proteome analysis to elucidate BMI1 specific interactome and RNA-Seq of BMI1 and selected candidates RYBP, CBX8 and PRP6 to underpin specific biological functions and RNA splicing modulation.

first: Verónica

last: Freire-Benéitez

first: Nicola

last: Pomella

first: Thomas

middle: O

last: Millner

first: Anaëlle

last: Dumas

first: Maria

middle: V

last: Niklison-Chirou

first: Eleni

last: Maniati

first: Jun

first: Vinni

last: Rajeeve

first: Pedro

last: Cutillas


title: Multi- and transgenerational disruption of maternal behavior and female puberty by Endocrine Disrupting Chemical (EDC) mixture exposure

city: Liege

first: David

last: Lopez Rodriguez

state: Liege

address: Avenue de l'Hopital 11

department: GIGA-Neuroscience

country: Belgium

institute: University of Liege

summary: We report gene expression profiles in the median basal hypothalamus of 21-day old female wistar rats from the F1 and F3 generation after exposure to a mixture of Endocrine Disrupting Chemicals or vehicle

overall_design: Expression analysis between EDC-exposed and control animals in the F1 and F3 generation

first: Carlos

middle: F

last: Alywin

first: Alejandro

last: Lomniczi


title: Early epigenetic changes precede genetic alterations and drive hepatocarcinogenesis

status: Public on Mar 01 2021

city: Mainz

first: Alicia

middle: Anna

last: Poplawski

state: Rhineland Palatinate

address: Obere Zahlbacher Straße 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics

country: Germany

institute: University Medical Center Johannes Gutenberg University Mainz

type: Methylation profiling by genome tiling array

summary: genome-wide methylome and transcriptome profiling of cirrhotic liver, low- and high-grade dysplastic lesions, eHCC and pHCC synchronouCLy detected in HCC patients with chronic hepatitis B infection. Identification of molecular epi-drivers by integrative analyses and validation in two independent cohorts comprising 933 HCC.

overall_design: A total of 28 samples were collected including 7 surrounding liver tissues, i.e. cirrhotic liver (CL), 4 low-grade dysplastic nodules (LGDN), 9 high-grade dysplastic nodules (HGDN), 5 early HCC (eHCC) and 3 progressed HCC (pHCC) from 8 HCC patients with chronic hepatitis B infection.

first: Carolin

last: Czauderna

first: Colm

middle: J

last: O’Rourke

first: Darko

last: Castven

first: Benjamin

last: Perez-Aguilar

first: Diana

last: Becker

first: Stephanie

last: Heilmann-Heimbach

first: Margarete

last: Odenthal

first: Wafa

last: Amer

first: H

last: Binder

first: Dirk

last: Ridder

first: Mario

last: Schindeldecker

first: Beate

middle: K

last: Straub

last: Galle

first: Jesper

middle: B

last: Andersen

first: Snorri

last: Thorgeirsson

first: Young

last: Nyun Park

first: Jens

middle: U

last: Marquardt


title: human ovarian cancer cells:parental PTX-sensitive cells (OVCAR-3) vs. PTX-resistant cells (OV3R-PTX)

status: Public on Mar 16 2021

city: Shanghai

first: GUOXIONG

last: XU

state: Shanghai

address: 1508 Longhang Road

department: Research Center for Clinical Medicine

institute: Jinshan Hospital of Fudan University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Transcriptional profiling (lncRNA and mRNA) of human ovarian cancer cells comparing parental PTX-sensitive cells (OVCAR-3) vs. PTX-resistant cells (OV3R-PTX, derived from OVCAR-3).

overall_design: Two-condition experiment, OVCAR-3 vs. OV3R-PTX cells. Biological replicates:3 replicates in each group.

first: Guoxiong

last: Xu

first: Lingyun

last: Zhang


title: The role of microRNAs in the pathogenesis of IgA nephropathy

status: Public on Feb 23 2021

city: Leicester

first: Izabella

middle: Zofia Anna

last: Pawluczyk

address: University Road

department: Cardiovascular Sciences

institute: University of Leicester

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the expression of microRNAs in renal biopsies from patients with IgA nephropathy (progressive form and non progressive form), membranous and thin membrane nephropathies

overall_design: RNA from each of six frozen renal biopsies from each of the 4 cohorts was extracted and sent to Exiqon for next generation sequencing

first: I

first: J

last: Barratt


title: Anti-inflammatory effect of grape proanthocyandins (PAC) in vitro.

status: Public on Feb 19 2021

first: Andrew

last: Williams

summary: PAC polymers of different degrees of polymerization (DP) were used to stimulate murine RAW macrophages.

overall_design: PAC polymers of different DP were purified from grape pomace. RAW 246.7 macrophages were either mock treated or stimulated with lipopolysaccahride (LPS), and then exposed to the different PAC polymers.


title: The protozoan inhibitor Atovaquone affects mitochondrial respiration and shows in vitro efficacy against glucocorticoid-resistant cells in childhood B-cell acute lymphoblastic leukaemia

status: Public on Feb 26 2021

city: Plovdiv

first: Yordan

last: Sbirkov

address: 15 A Vassil Aprilov Blvd

department: Medical Biology

country: Bulgaria

institute: Medical University of Plovdiv

summary: Atovaquone is a well-tolerated drug used in the clinic mainly against malaria. Being a ubiquinone analogue, this drug inhibits co-enzyme Q10 of the electron transport chain (ETC) affecting oxidative phosphorylation and cell metabolism. In this study we tested the effect of Atovaquone on cALL cells in vitro.  The outcome of this inhibition of the ETC is a marked decrease in basal respiration and ATP levels, as well as reduced proliferation, cell cycle arrest and induction of apoptosis. On the transcriptional level, we see changes in cellular metabolic processes, activation of p53 pathway, apoptosis, enrichment of cell cycles genes and downregulation of hypoxia and mTORC1 signalling pathway.

overall_design: Comparing biological triplicates of untreated and treated with Atovaquone REH cells (72h).


title: Pore-forming toxin alpha-hemolysin efficiently improve the immunogenicity and protective efficacy of protein antigens by increasing antigen uptake and targeting ADAM10

status: Public on Feb 20 2021

city: Chongqing

first: Jintao

last: Zou

state: China

address: Gaotanyanstreet

institute: Army Medical University

summary: Highly immunogenic exotoxins were proved to be efficient in improving the immunogenicity of polysaccharides, traditionally known as carrier proteins. However, the efficacy of exotoxins on protein antigens remains to be excluded. In the current study, the candidate antigen PA0833 from Pseudomonas aeruginosa was fused to the α-hemolysin mutant HlaH35A from Staphylococcus aureus. After immunization with the fusion protein, increased titers of PA0833-specific antibodies and higher protective efficacy were observed, companied with decreased bacterial burden and pro-inflammatory cytokines secretion when compared with PA0833 immunization alone. Then, by using fluorescently labeled antigens to track antigen uptake and delivery, we found that fusion to HlaH35A significantly improved antigen uptake in injected muscles and antigen delivery to draining lymph nodes. Both in vivo and in vitro studies demonstrated that increased antigen uptake by fusion to HlaH35A were mainly mediated by monocytes and macrophages in a macropinocytosis dependent manner, probably due to targeting ADAM10, the host receptor of Hla. Further, transcriptome analysis was performed and the result showed that several immune signaling pathways were activated by HPF, which also shed light on the mechanism of improved immunogenicity. Finally, improvement of immunogenicity by fusion to HlaH35A was also confirmed in two other anigens, GlnH from Klebsiella pneumoniae and the model antigen OVA, which indicated that HlaH35A could serve as a universal carrier protein to improve the immunogenicity of protein antigens.

overall_design: mRNA profiles of Raw264.7 cell at 6-hours post treated with His buffer, PA0833, Hla-PA0833(HPF)

first: Jinyong

first: Quanming


title: Single Cell RNA Sequencing Analysis of WT and CD169-DTR Adipose Tissue Vascular Fraction

status: Public on Mar 19 2021

city: SINGAPORE

first: JIA CHI

last: TAN

address: 8a Biomedical Grove

institute: SIgN

summary: Using t-distributed stochastic neighbor embedding (t-SNE) analysis, we identified 23 transcriptionally distinct cell clusters which are present in the eWAT when the four experimental groups were combined (ND and HFD with AMTs or without).Our analysis identifies six main cell clusters of CD45- cells: two adipocyte stem cell fractions (ASC1 and ASC2), stromal cells, two fractions of vascular endothelial cells (VEC1 and VEC2) as well as a population showing a gene signature for of mesothelial cells, among the CD45+ cells, seventeen lymphoid and myeloid cell subpopulations are detectable in the eWAT ranging from monocytes, monocyte-derived macrophages, dendritic cells, eosinophils, mast cells, B cells, CD4+ Th2, CD4+ Th17, Tregs and CD8+ T cells, NK cells, NKT cells In obese mice, one week absence of ATM in the eWAT affected mostly the non-haematopoetic cell compartment, while the total number of cell clusters and percentage of haematopoetic CD45+ cells were maintained roughtly the same between the four experimental groups, whereas ablation of ATMs in lean mice did not perturb dramatically the cluster distribution of CD45- cells.

overall_design: To investigate the effects of ablation tissue resident macrophages on immune and non-immune cells in adipose tissue under both lean and obese conditions, WT and CD169-DTR mice were fed with Normal Diet or High Fat Diet for 16 weeks, followed by Diphtheria Toxin (DT) treatment for 7 days to ablate tissue resident macrophages. Epidimal adipose tissue were processed to get the stromal vascular fraction cells. CD45+ and CD45- cells (exclude the high proportion of F4/80hi cells as well as Ly6Chi monocytes) were sorted separately and combined with a raton of 1:1 for sequencing analysis.

first: Christiane

last: Ruedl

first: Qi

last: Chen


title: Altered hippocampal transcriptome dynamics following sleep deprivation

city: Iowa City

first: Ethan

last: Bahl

state: IA

address: 25 S Grand Ave

institute: University of Iowa

summary:
Purpose: To comprehensively identify the gene expression changes that occur after acute sleep deprivation.
Method: We performed total RNA sequencing after 5hours of sleep deprivation.
Results: Using total RNA-sequencing, we show that acute sleep deprivation causes dramatic gene expression changes in the mouse hippocampus.
Conclusion: This study provides insight into the biological impact of acute sleep deprivation.

overall_design: Whole hippocampus RNA profiles of 2-4 months old male C57Bl/6J mice who were either sleep deprived for 5hours or left undisturbed.

first: Marie

middle: E

last: Gaine

first: Snehajyoti

last: Chatterjee

first: Jacob

last: Michaelson

first: Ted

last: Abel

first: Lisa

middle: C

last: Lyons


title: Cardiac-specific deletion of voltage dependent anion channel 2 leads to dilated cardiomyopathy by altering calcium homeostasis

city: Salt Lake City

first: Stavros

middle: George

last: Drakos

state: Utah

address: 95 South 2000 East

department: Cardiovascular research and training institute

institute: University of Utah

summary: Voltage dependent anion channel 2 (VDAC2) is an outer mitochondrial membrane porin known to play a significant role in apoptosis and calcium signaling. Abnormalities in calcium homeostasis often leads to electrical and contractile dysfunction and can cause dilated cardiomyopathy and heart failure. However, the specific role of VDAC2 in intracellular calcium dynamics and cardiac function is not well understood. To elucidate the role of VDAC2 in calcium homeostasis, we generated a cardiac ventricular myocyte-specific developmental deletion of Vdac2 in mice. Our results indicate that loss of VDAC2 in the myocardium causes severe impairment in excitation-contraction coupling by altering both intracellular and mitochondrial calcium signaling. We also observed adverse cardiac remodeling which progressed to severe cardiomyopathy and death. Reintroduction of VDAC2 in 6-week-old knock-out mice partially rescued the cardiomyopathy phenotype. Activation of VDAC2 by efsevin increased cardiac contractile force in a mouse model of pressure-overload induced heart failure. In conclusion, our findings demonstrate that VDAC2 plays a crucial role in cardiac function by influencing cellular calcium signaling. Through this novel role in cellular calcium dynamics and excitation-contraction coupling VDAC2 emerges as a plausible therapeutic target for heart failure.

overall_design: 16-week old VDAC2 KO vs VDAC2 WT Cardiac tissue

first: S

middle: G


title: Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA

status: Public on Feb 16 2021

city: Illkirch

first: Fang

last: WANG

address: Parc d'Innovation 1, Rue Laurent Fries Illkirch, 67404

country: France

institute: INSTITUT DE GENETIQUE DE BIOLOGIE MOLECULAIRE ET CELLURAIRE (IGBMC)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [RNA-Seq]

summary: The deubiquitinating module (DUBm) of mammalian SAGA complex is composed of the ubiquitin-specific protease 22 (USP22) and ATXN7, ATXN7L3 and ENY2 adaptor proteins, which are all needed for the full activity of USP22 enzyme. In addition, ATXN7L3 is critical for directing the DUB module substrate specificity towards H2Bub1. We reported that USP22 and ATXN7L3 are essential for normal embryonic development of mice, however their requirements are not identical during this process. Global histone H2Bub1 levels were only slightly affected in Usp22 null embryos, while in contrast H2Bub1 levels were strongly increased in Atxn7l3 null mutants and derived cellular systems. Interestingly, the strong H2Bub1 increases observed in the Atxn7l3-/- mouse embryonic stem cells, or Atxn7l3-/- mouse embryonic fibroblasts, do not correlate with the modest genome-wide Pol II occupancy changes observed in the two knock-out cellular systems. Thus, histone H2Bub1 deubiquitylation does not directly regulate global RNA polymerase II transcription.

overall_design: Genome-wide investigation of the role of H2Bub in mouse embryonic stem cells (mESCs) and mouse primary embryonic fibroblasts (MEF) cells

last: Wang

first: Farrah

last: El-Saafin

first: Tao

last: Ye

first: Mathieu

last: Stierle

first: Matej

last: Durik

first: Veronique

last: Fischer

first: Didier

last: Devys

first: Stéphane

last: Vincent

first: László

last: Tora


title: Gene expression profile of epidermis from psoriasis lesions and healthy controls

status: Public on Feb 09 2021

city: guangzhou

first: dan

last: hong

address: 107 Yanjiang Rd W, Guangzhou, China

department: Department of Dermatology

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

summary:
Psoriasis is characterized by hyperplasia and disrupted differentiation of keratinocytes. Keratinocytes are considered not only the target but also the critical participants.
To explore the role of keratinocytes in psoriasis, we used microarrays to compared gene expression profile of epidermis between psoriasis lesions and healthy normal skin.

overall_design: In this study,we seperated epidermis from psoriasis lesions and healthy normal skin(n=4 for each group) and extract total RNA for genome microarray .

first: Zhenrui

last: Shi


title: Microarray comparative analysis of wild-type and hd1-3 mutant rice

status: Public on Feb 04 2021

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

summary: Heading date1(Hd1) is a critical regulator controlling rice flowering time, which promotes flowering under short-day (SD) conditions and represses flowering under long-day (LD) conditions. In our previous study (Luan et al., 2009), we identified a rice mutant, hd1-3, in which the Hd1 gene was deficient due to several insertions/deletions in the coding region. To search for downstream genes regulated by Hd1, we performed microarray analysis of hd1-3 mutant and the wild-type Zhonghua11  under both SD and LD conditions. According to the microarray results, SDG712 gene was significantly downregulated in the hd1-3 mutant, indicating that SDG712 gene may acts downstream of Hd1, and may functions in rice flowering time regulation.

overall_design: The leaves of 35-day-old plants of hd1-3 mutant and the wild-type Zhonghua11 grown under SD and LD conditions were collected.  Total RNAs were extracted using TRIzol and mRNAs were purified for microarray analysis.

first: Siju

last: Zhang

first: Weijiang

last: Luan


title: STAT3 maintains skin barrier integrity by modulating SPINK5 and KLK5 expression in keratinocytes

status: Public on Feb 05 2021

city: Seoul

first: Jaehyung

last: Kim

address: 46, Gaeunsa 2-gil, Seongbuk-gu, Seoul, Korea

country: South Korea

institute: KoreaUniversity

summary: We elucidated the potential role of STAT3 in the skin barrier and its effect on kallikrein-related peptidase 5 (KLK5) and serine protease inhibitor Kazal-type 5 (SPINK5) expression using a mouse model with keratinocyte-specific ablation of STAT3.


title: Transcriptome profiling of spinal motor atrophy mice skeletal muscle tissue

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

summary: Spinal motor atrophy mice (SMN delta 7 mice) and wild-type control hindlimb skeletal muscle tissue was used for transcriptome profiling by mRNA-seq.

overall_design: Total RNA was used as input for Stranded mRNA library preparation.  Sequencing libraries were sequenced for depth greater than 50 million reads and differential expression analysis was conducted using normalized counts with log 2 fold-change and adjusted p-value cutoffs for filtering.

first: Clifton

middle: L

last: Dalgard

first: Nikki

last: McCormack

first: Barrington

last: Burnett

middle: R


title: Gene expression analysis comparing between pure- and mixed type testicular seminoma

city: Tokorozawa

first: Kosuke

last: Miyai

state: Saitama

address: Namiki 3-2

department: Basic Pathology

institute: National Defense Medical College

summary: We hypothesized that the comparison between pure type seminoma and seminoma components in mixed tumor (mixed type seminoma) could reveal early changes of the reprogramming process; however, only a little data is available. We performed gene expression microarray analysis of 6 pure type and 6 mixed type seminomas, and the hierarchical clustering analysis properly grouped each type of seminomas into a separated cluster. Supervised analysis between these groups identified 154 significantly dysregulated genes (Storey-adjusted q < 0.05). The genes with the highest overexpression in mixed type seminomas compared with the pure type seminomas included MT1 isoforms, PRSS8, TSC22D1, and SLC39A4; down-regulated genes included DEFB123, LMTK2, and MTRF. Functional annotation analysis of the differently expressed genes revealed the top-ranking categories related to cellular zinc metabolism, consisting of MT-1 isoforms and SLC39A4.

overall_design: Twelve cases of primary testicular germ cell tumor, consisting of 6 pure seminomas and 6 mixed tumors with seminoma and non-seminomatous components, were identified from the files of the Department of Laboratory Medicine, National Defense Medical College Hospital. All the cases were surgically resected specimens obtained from 2015 to 2019.

first: Keiichi

last: Ito

first: Susumu

last: Matsukuma

first: Hitoshi

last: Tsuda


title: Rerep-Seq of copper resistant yeast

status: Public on Feb 01 2021

city: Aurora

first: Joshua

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

summary: NOT PROVIDED; REQUESTED

overall_design:
In this study we compared genome wide re-replicated DNA sequencing of copper resistant yeast vs untreated controls
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Philip

last: Tatman

first: Gregory

last: Wright


title: Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [ChIP-seq]

status: Public on Feb 02 2021

city: Beijing

first: Wei

last: Li

address: 1st Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Chromatin remodeling plays very important role in cell reprogramming, but its underlying  mechanism remains poorly understood. Here, we show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the other two stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to  their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene  network establishment. Our results not only uncover a previously unknown function of RNF20-  mediated H2B ubiquitination in cell reprogramming, but also provide mechanistic insights into  the epigenetic regulation of reprogrammable cells.

overall_design: Examination of SOX2 inRnf20-/- reprogrammable cells and Rnf20+/+ reprogrammable cells.

first: Liying

last: Wang

first: Chao

last: Liu

first: Zhiliang

last: Xu

first: Libin


title: Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming [RNA-seq]

summary: Chromatin remodeling plays very important role in cell reprogramming, but its underlying mechanism remains poorly understood. Here, we show that RNF20 is highly expressed at the early stage of reprogramming along with the accumulation of H2B ubiquitination at the same stage, and Rnf20 knockout results in the failure of reprogramming at the initial stage but not the other two stages. RNA-seq showed that Rnf20 knockout mainly affects the early stage of cell reprogramming by impairing the transcription of MET-related genes and early pluripotency genes. Importantly, Rnf20 knockout results in a more compacted chromosomes structure in reprogrammable cells, suppressing the recruitment of reprogramming transcription factors to their proper locations on the chromosomes, and finally resulting in the failure of pluripotent gene network establishment. Our results not only uncover a previously unknown function of RNF20-mediated H2B ubiquitination in cell reprogramming, but also provide mechanistic insights into the epigenetic regulation of reprogrammable cells.

overall_design: The transcriptome of Rnf20-/- cells and Rnf20+/+ cells at day 3 of OSKM reprogramming


title: Histone H2B ubiquitination mediated chromatin relaxation is essential for the induction of somatic cell reprogramming.


title: Annotation- and Batch Effect Correction in TCGA IsomiR Expression Data [Third-party re-analysis]

status: Public on Feb 17 2021

city: Heidelberg

first: Susanne

last: Ibing

address: Berliner Straße 41

department: Applied Bioinformatics

institute: German Cancer Research Center

type:
Other
Third-party reanalysis

summary: The Cancer Genome Atlas (TCGA) Isoform Expression Quantification Data is the largest ressource of isomiR level sequenced cancer data publicly available. Since the datasets were built up over years and through different contributing institutions, it is not free of batch effects. We evaluated different batch correction approaches to remove batch effects in the data, details of the best performing algorithm and batch variables are included in the supplementary file. Additionally, annotation of the chromosomal end position of each isomiR feature was corrected by the offset of 1 to account for exclusive annotation.

overall_design:
Limma/ComBat batch corrected isomiR expression data for 16 TCGA Projects.

Please note that Sample metadata is added as a Series supplementary file which lists links to  the GDC legacy portal/GDC harmonized data portal and their associated processed data files.

re-analysis data processing step:
Download of TCGA IsomiR Expression Quantification data (here: normalized expression [RPM] will be used)
Feature annotation correction: end position -1
Filtering for sequencing depth: exclude samples with sequencing depth < 1000000 total mapped reads
For the *_tumor_FILTER.txt files: exclude normal samples from analysis
IsomiR expression filter: excluding isomiRs with no expression amongst all remaining samples in the cohort (sum 0 filter) or median expression below 15 RPM (median 15 filter)
Batch correction using the ComBat function (sva R package, version 3.32.1) or removeBatchEffects function (limma R package, version 3.40.6). Different batch variables were used for sequential batch correction, optimal combination of batch correction algorithm and batch variables was chosen after evaluation of success of batch correction. Sample information for batch effect correction available in supplementary file.
genome build: GRCh38
*.txt files including batch corrected isomiR expression data of different TCGA cohorts after (different) filtering steps

first: Birgitta

last: Michels

first: Moritz

last: Mosdzien

first: Helen

last: Meyer

first: Lars

last: Feuerbach

first: Cindy

last: Koerner


title: Rerep-Seq of cadmium resistant breast cancer MDA-231 cells

summary: NOT PROVIDED; REQUESTED

overall_design: In this study we compared genome wide re-replicated DNA sequencing of cadmium resistant MDA-231 breast cancer cells vs untreated controls


title: Next Generation Sequencing Facilitates Quantitative Analysis of TRPM1 overexpression and vector control in 661W cell Transcriptomes

status: Public on Jan 29 2021

city: Tainan

first: Che-Hung

last: Shen

state: Taiwan

address: No. 367, Sheng-Li Rd.,, North Dist.,

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

summary:
Purpose: The goal of this study are to investigate the TRPM1-regulated genes using RNAseq to compare the transcriptome profiling between 661W cells  expressing TRPM1 and control vectors
Methods: RNAs were isolatedusing the RNeasy Mini kit (Qiagen). RNA-seq libraries were prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) and validated using the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). Libraries were sequenced on a NovaSeq 6000 sequencer (Illumina, CA, USA). Clean reads were aligned to the mouse genome (GRCm38) using HISAT2 (version 2.1.0) after removing low-quality reads. The differential expression of genes between TRPM1-overexpression and control cells was computed using the fragments per kilobase of transcript per million mapped reads calculated by featureCounts (version 2.0.0). Raw read counts were imported into edgeR (version 3.28.1) and analyzed by using R package of DESeq (version 1.40.0). Genes with false discovery rate (FDR) p-value < 0.05 adjusted by using Benjamini–Hochberg (BH) method were considered as differentially expressed genes (DEGs). Gene set enrichment analysis of the genes differentially expressed upon TRPM1 expression was done using the Gene Set Knowledgebase（GSKB）hallmark gene sets.
Results: We had 40,922,040 clean reads in the control group and 44,244,608 clean reads in the TRPM1-overexpressing group. We mapped 43,253, 668 (97.76%) sequence reads in the control group and 39,942,649 (97.6%) sequence reads in the TRPM1-overexpressing group. We identified 16,014 transcripts. 76 transcripts showed differential expression between the vector control group and TRPM1-expressing group, with a fold change ≥1.5 and p value <0.01. Gene set enrichment analysis of the genes differentially expressed upon TRPM1 expression uncovered several TRPM1-regulated genes that may contribute to photoreceptor function, such as retina morphogenesis and JAK-STAT cascade.
Conclusions: Our study represents the genes associated with TRPM1 overexpression in 661W photoreceptor cells using RNA-seq approach. The overexpression of  TRPM1 may contribute to regulate the photoreceptor morphogenesis and function

overall_design: RNAs isolated from 661W cells stably expressing 3xFlag-TRPM1 or control vector were subjected to RNAseq and gene set enrichment analysis


title: A Dinucleotide-barcode reporter system and application in dissecting the causal rule of regulatory risk SNPs

status: Public on Jan 30 2021

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

institute: Shandong University

type: Genome variation profiling by high throughput sequencing

summary: We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified prostate cancer-risk SNPs, we found 32, 9, and 11 regulatory SNPs in 22Rv1, PC-3, and LNCaP cells. Further mechanism study indicates that one SNP regulates gene expression in prostate cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting prostate cancer patients with prognostic prediction.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Blank DiR-seq bias analysis in LNCaP cell lines (3 replicates), Input plasmid library 10lib before transfection (3 replicates). Blank DiR-seq report analysis in LNCaP and MCF7 cell lines (3 replicates, respectively), Input plasmid library before transfection (3 replicates). SNP DiR-seq report analysis in 22Rv1, PC-3 and LNCaP cell lines (3 replicates, respectively), Input plasmid library before transfection (2 replicates).

first: Naixia

last: Ren

first: Bo

first: Qingqing


title: A neuroanatomical mechanism linking perinatal chemical exposure to prostate smooth muscle hyperactivity and altered voiding function

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

summary: The historical focus of male lower urinary tract dysfunction (LUTD) has been benign prostatic enlargement and other aging-related processes. Little attention has been directed towards the influence of early life events on urinary physiology in advancing age. Here, we identify the intrauterine environment as a modifier of adult voiding function and risk factor for male LUTD. To model environmental chemical exposures, we exposed pregnant mice to the environmental contaminant 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD, 1 µg/kg), coinciding with initiation of lower urinary tract development in male fetuses. Fetal TCDD exposure incites abnormal urodynamics in adult male mice, including increased urinary voiding frequency. TCDD also enhances adult prostate sensitivity to electrically evoked muscle contraction, suggesting increased autonomic tone. IUL TCDD exposure stably increases noradrenergic axon density beginning in the fetal period and persisting into adulthood. These changes are accompanied by increased abundance of a neurotrophin, Artemin (Artn), in the fetal prostate. This is the first evidence that intrauterine chemical exposures can reprogram prostate neuroanatomical development and drive prostatic smooth muscle hyperactivity in adulthood, which may create a susceptible phenotype for aging-related male lower urinary tract dysfunction.

overall_design: Embryonic day (E) 13.5 C57BL/6J mice were dosed in utero with TCDD (1 microgram/kg maternal dose) or corn oil vehicle (control, 5 mL/kg). Urogenital sinuses were collected at E16.75, mesenchyme removed by trypic digestion and dissection, and the underlying epithelium (UGE) isolated for sequencing. Each treatment group consisted of 4 biological replicates and each replicate contained 5 or 6 individual UGEs that were pooled for RNA isolation.

first: Cheryl

last: Dunham

first: Andrew

last: Schneider

first: Joseph

last: Gawdzik

first: Anne

last: Turco

first: Chad

middle: M

last: Vezina

first: Robyn

last: Tanguay

first: Richard

last: Peterson


title: Autoantibodies in sera from Sjogren's syndrome mice

status: Public on Jan 25 2021

city: Dallas

first: Chengsong

last: Zhu

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

summary: We performed autoantigen arrays on sera derived from Sjogren's syndrome mice that lacked Myd88 systemically (NOD.B10LSL-/- strain) or lacked Myd88 in specific tissues (NOD.B10Myd88delta and NOD.B10LSL-/-Vav+ strains). We also examined sera from Myd88-sufficient controls (NOD.B10Myd88fl/fl, NOD.B10, and NOD.B10LSL+/- strains).

sample_organism:
Mus musculus
blank sample

overall_design: We first compared sera from NOD.B10Myd88fl/fl mice (n = 5) to NOD.B10Myd88delta mice(n = 5). We then performed arrays using sera from NOD.B10, NOD.B10LSL+/-, NOD.B10LSL-/-, and NOD.B10LSL-/-Vav+ mice.

first: Jill

last: Kramer


title: Comparative RNAseq analysis of Trypanosoma brucei and T. congolense

status: Public on Jan 22 2021

city: Midlothian

first: Pieter

last: Steketee

address: Easter Bush Campus

department: Division of Infection and Immunity

institute: Roslin Institute, University of Edinburgh

summary:
Purpose: The is a major paucity of knowledge regarding the biology of Trypanosoma congolense, a protozoan parasite primarily responsible for Animal African Trypanosomiasis. In contrast, the closely related species T. brucei, is far better understood. To characterise core metabolism in T. congolense, comparative RNAseq analysis was undertaken to assess similarities and differences in transcript levels of genes associated with metabolism
Methods: Samples from both in vitro culture and ex vivo (isolated from murine infections) bloodstream-form T. brucei and T. congolense were RNA-sequenced. Data was analyzed using a pipeline that allows for inter-species comparison
Results: T. congolense exhibits increased transcript abundance in genes associated with the glycosomal succinate shunt, as well as mitochondrial metabolism, in particular the catabolism of pyruvate to acetate, compared to T. brucei. These differences occur both in vitro and ex vivo. Furthermore there are differences in nucleotide metabolism, and transcript levels of genes involved in fatty acid synthesis are reduced in T. congolense compared to T. brucei.
Conclusions: Comparative RNAseq between two closely related species provided a detailed overview of similarities and differences in core metabolism. This carries significant implications for adaptation to in vitro culture, and drug efficacy, mode of action and mode of resistance.

sample_organism:
Trypanosoma brucei
Trypanosoma congolense

overall_design: 4 replicates per sample group, 4 sample groups, 2 species (T. brucei and T. congolense), 2 conditions (in vitro and ex vivo)

first: Emily

middle: A

last: Dickie

first: James

last: Iremonger

first: Kathryn

last: Crouch

first: Edith

last: Paxton

first: Siddarth

last: Jayaraman

first: Omar

last: Alfituri

first: Georgina

last: Awuah-Mensah

first: Ryan

last: Ritchie

first: Achim

last: Schnaufer

first: Harry

middle: P

last: de Koning

first: Catarina

last: Gadelha

first: Bill

last: Wickstead

first: Michael

last: Barrett

first: Liam

last: Morrison


title: M16-106 adult and pediatric ALL clinical trial - RNAseq dataset

city: North Chicago

first: Xin

last: Lu

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: Combining venetoclax, a selective BCL-2 inhibitor, with low-dose navitoclax, a BCL-XL/BCL-2 inhibitor, may potentiate therapeutic BCL-2 and BCL XL inhibition without dose-limiting thrombocytopenia associated with navitoclax monotherapy. The safety and preliminary efficacy of venetoclax with low-dose navitoclax and chemotherapy was assessed in this phase 1 dose escalation study (NCT03181126) in pediatric and adult patients with relapsed/refractory acute lymphoblastic leukemia or lymphoblastic lymphoma. Forty-seven patients received treatment. A recommended phase 2 dose of 50 mg navitoclax for adults and 25 mg for patients <45 kg with 400 mg adult-equivalent venetoclax was identified. Delayed hematopoietic recovery was the primary safety finding. The complete remission rate was 60%, including responses in patients who had previously received hematopoietic cell transplantation or immunotherapy. Thirteen (28%) patients proceeded to transplantation or CAR T-cell therapy on study. Venetoclax with navitoclax and chemotherapy was well tolerated and had promising efficacy in this heavily pretreated patient population.

overall_design: The M16-106 trial tested Venetoclax in combination with Navitoclax in adult and pediatric patients with relapsed/refractory ALL. Tumor samples were collected at baseline, total stranded transcriptome sequencing was performed using the TruSeq Stranded Total RNA library preparation kit and sequencing performed using HiSeq 4000 and NovaSeq 6000 platforms (Illumina). The low input RNA library preparation kit (NuGen Ovation V2) was used for samples with limiting material.


title: Histone H2Bub1 deubiquitylation is essential for mouse development, but does not regulate global RNA [ChIP-Seq]

first: Fang

last: WANG

last: Wang

first: Farrah

last: El-Saafin

first: Tao

last: Ye

first: Mathieu

last: Stierle

first: Matej

last: Durik

first: Veronique

last: Fischer

first: Didier

last: Devys

first: Stéphane

last: Vincent

first: László

last: Tora


title: A novel chemical inhibitor TXX sequencing, Jun 20 '20

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

summary: To investigate the corelation of genes regulated by TXX-1-10 and Rimonabant , we treated MDA-MB-231 cells with TXX-1-10 and Rimonabant.

overall_design: MDA-MB-231 cells with TXX-1-10 and Rimonabant treatment


title: HoxB genes regulate neuronal delamination in the trunk neural tube by controlling the expression of Lzts1

status: Public on Jan 18 2021

city: Marseille

first: Andrew

last: Saurin

address: Campus de Luminy

institute: IBDM / CNRS

summary: Differential Hox gene expression is central for specification of axial neuronal diversity in the spinal cord. Here, we uncover an additional function of Hox proteins in the developing spinal cord, restricted to B cluster Hox genes. We found that members of the HoxB cluster are expressed in the trunk neural tube of chicken embryo earlier than Hox from the other clusters, with poor antero-posterior axial specificity and with overlapping expression in the intermediate zone (IZ). Gain-of-function experiments of HoxB4, HoxB8 and HoxB9, respectively representative of anterior, central, and posterior HoxB genes, resulted in ectopic progenitor cells in the mantle zone. The search for HoxB8 downstream targets in the early neural tube identified the Leucine Zipper Tumor Suppressor 1 gene (Lzts1), which expression is also activated by HoxB4 and HoxB9. Gain and loss of function experiments showed that Lzts1, expressed endogenously in the IZ, controls neuronal delamination. These data collectively indicate that HoxB genes have a generic function in the developing spinal cord, controlling the expression of Lzts1 and neuronal delamination.

overall_design: Neural tube in ovo electroporations were performed at HH11. Two pCIG controls and Two Hoxb8-pCIG experiments were performed. GFP-expressing cells were FACS-isolated and total polyA RNA sequenced

first: Axelle

last: Wilmerding

first: Lucrezia

last: Rinaldi

first: Nathalie

last: Caruso

first: Laure

last: Re

first: Emilie

last: Bonzom

first: Yacine

last: Graba

first: Marie-Claire

last: Delfini


title: Elucidation of an anaerobic pathway for metabolism of L-carnitine-derived γ-butyrobetaine to trimethylamine in human gut bacteria

status: Public on Feb 03 2021

city: Cambridge

first: Lauren

middle: Julia

last: Rajakovich

state: MA

address: 12 Oxford Street

department: Chemistry & Chemical Biology

institute: Harvard University

summary: Trimethylamine (TMA) is an important gut microbial metabolite strongly associated with human disease. There are prominent gaps in our understanding of how TMA is produced from the essential dietary nutrient L-carnitine, particularly in the anoxic environment of the human gut where oxygen-dependent L-carnitine-metabolizing enzymes are likely inactive. Here, we elucidate the chemical and genetic basis for anaerobic TMA generation from the L-carnitine-derived metabolite γ-butyrobetaine (γbb) by the human gut bacterium Emergencia timonensis. We identify a set of genes upregulated by γbb and demonstrate that the enzymes encoded by the induced γbb utilization (bbu) gene cluster convert γbb to TMA. The key TMA-generating step is catalyzed by a previously unknown type of TMA-lyase enzyme that utilizes a flavin cofactor to catalyze a redox neutral transformation. We identify additional cultured and uncultured host-associated bacteria that possess the bbu gene cluster, providing insights into the distribution of anaerobic γbb metabolism. Lastly, we present genetic, transcriptional, and metabolomic evidence that confirms the relevance of this metabolic pathway in the human gut microbiota. These analyses indicate that the anaerobic pathway is a more substantial contributor to TMA generation from L-carnitine in the human gut than the previously proposed aerobic pathway. The discovery and characterization of the bbu pathway provides the critical missing link in anaerobic metabolism of L-carnitine to TMA, enabling investigation into the connection between this microbial function and human disease.

overall_design: RNA-Seq of Emergencia timonensis SN18 cultured with vehicle, γ-butyrobetaine, DL-carnitine, or GABA

first: Beverly

last: Fu

first: Maud

last: Bollenbach

first: Emily

last: Balskus


title: Activation of γ-globin gene expression by GATA1 and NF-Y in hereditary persistence of fetal hemoglobin

status: Public on Apr 22 2021

city: Memphis

first: Mitchell

middle: J.

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

summary: Naturally occurring mutations in the Î³-globin promoters can result in hereditary persistence of fetal hemoglobin (HPFH), a benign condition that ameliorates the severity of Î²-hemoglobinopathies through increased post-natal fetal hemoglobin (HbF) expression. Mutations in the Î³-globin promoters result in loss or de novo recruitment of transcription factors, yet the cis-regulatory elements involved in Î³-globin transcription in the context of HPFH are not clearly defined. We demonstrate that the -115 cluster of HPFH mutations require GATA1 binding to at -186 in cooperation with NF-Y at the proximal CCAAT box at -85 for Î³-globin expression. We show that multiple HPFH mutations increase HbF in an erythroid cell line and result in GATA1 binding at -186. Mutation of the -186 GATA motif in HPFH erythroid cell lines and erythroid-differentiated CD34+ cells resulted in loss of GATA1 binding and reduction in fetal hemoglobin. NF-Y ChIP-seq in HPFH erythroid cell lines demonstrated binding to the proximal CCAAT box at -85 was also found to be critical for HPFH-mediated Î³-globin expression. Together, the -186 GATA motif and -85 proximal CCAAT box function in an additive and independent manner. Our results reveal detailed evidence for common, positive acting cis-regulatory elements that may provide more general mechanisms for erythroid gene expression.

overall_design:
ChIP-seq experiments were performed in HUDEP-2 cells harboring mutations in the γ-globin promoter for GATA1 and NF-YB. Input samples were used as control
ATAC-seq experiments were performed in undifferentiated HUDEP-2 cells harboring mutations in the -115 CCAAT box of the γ-globin promoter.
Hi-C experiments were performed in WT and single HBG allele HUDEP-2 cells

first: P

last: Doerfler

first: M

middle: J


title: Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

status: Public on Jan 13 2021

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

summary: The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.

overall_design: Cut&Run on SNU398 cells, 3 replicates for both SALL4 and IgG. RNA-Seq on SNU398 cells post SALL4 knockdown.

first: Nikki

last: Kong

first: Hong

middle: K

last: Tan

first: Jesse

middle: V

last: Kurland

first: Kol Jia

last: Yong

first: John

last: Young

first: Yang

last: Yang

first: Fudong

last: Li

first: Jonathan

last: Lee

first: Yue

last: Liu

first: Chan-Shuo

last: Wu

first: Alicia

last: Stein

first: Hongbo

last: Luo

first: Leslie

last: Silberstein

first: Martha

last: Bulyk

first: Li

last: Chai

first: Daniel

last: Tenen


title: Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth ssing sterol requirements enables anaerobic growth of the thermotolerant yeast Kluyveromyces marxianus

status: Public on Jan 06 2021

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

department: Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: Analysis of gene expression changes in S. cerevisiae and K. marxianus in response to oxygen-limitation

sample_organism:
Kluyveromyces marxianus
Saccharomyces cerevisiae

overall_design: 18 samples (comprising 5 pairwise comparisons), two biological replicates per sample

first: Wijb

last: Dekker

first: Raul


title: Transcriptomic analyses of the liver in female mice exposed to 1,4-dioxane in drinking water

status: Public on Jan 21 2021

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

summary: We evaluated liver tissues of B6D2F1/Crl mice exposed to 0, 40, 200, 600, 2000, or 6000 ppm 1,4-dioxane in drinking water for 7, 28, or 90 days in support of an investigation of the mode of action for 1,4-dioxane-induced murine liver tumors. TempO-Seq technology was used to measure global hepatic gene expression.  Exposure-induced transcriptional responses increased by dose and exposure duration, with few differentially expressed genes at 40 and 200 ppm regardless of exposure duration. Pathway enrichment analysis identified significant perturbations in pathways associated with xenobiotic metabolism, complement and coagulation cascades and fatty acid metabolism in 600, 2000, and 6000 ppm groups at all timepoints compared to time-matched control groups. A significant transcriptomic proliferative response was only observed in 6000 ppm exposed mice at 90 days. Differential gene expression and pathway enrichment analysis results suggest 600 ppm as a potential threshold concentration for hepatic transcriptomic response to 1,4-dioxane in female mice.

overall_design: RNA sequencing data were used to examine the transcriptomic response in the livers of female mice exposed to 1,4-dioxane in the drinking water by comparing liver tissue from 6 treatment groups at 3 different timepoints.

first: Grace

last: Chappell

first: Laurie

middle: C

last: Haws

first: Joanna

last: Klapacz

first: Matthew

last: LeBaron

first: Robert

last: Budinsky

first: Rachel

last: Golden


title: Single cell level analysis of the Arabidopsis root transcriptome and chromatin accessibility

status: Public on Jan 11 2021

city: Santa Fe

first: Andrew

middle: D

last: Farmer

state: NM

address: 2935 Rodeo Park Dr E

institute: NCGR

summary: The nuclei of Arabidopsis root seedlings were isolated then use to establish a single cell level resolution transcriptome (sNucRNA-seq) and profile of chromatin accessibility (sNucATAC-seq) applying 10X Genomics technologies.

overall_design: The nuclei of the root of 7 days-old Arabidopsis seedlings grown on agar MS medium were isolated. Upon isolation, the nuclei suspension was used to create sNucRNA-seq and sNucATAC-seq libraries. Five and two independent replicates were generated to perform these experiments., respectviely. The libraries were sequenced using high-throughput sequencing technologies. The data were analyzed using CellRanger, Seurat and Signac.

first: Sandra

last: Thibivilliers

first: Kook

middle: H

last: Ryu

first: John

last: Schiefelbein

first: Marc

last: Libault


title: The Atypical Antipsychotic Risperidone Targets Central Melanocortin 4 Receptors to Cause Weight

status: Public on Jan 01 2021

first: Li

last: Li

address: 5323 Harry Hines Boulevard

summary: hypothalami from female C57BL/6 mice fed either the risperidone or the control diet for 28 days, along with those from a third group of “pair-fed” mice that were given the risperidone diet, but limited to the same amount that Ctrl_ Ad lib mice had consumed.

overall_design: Ctrl_Ad.lib, n=7; RIS_Ad lib, n=7; RIS_PF, n=6

first: Chen

last: Liu


title: Ketogenic Diet dependent Immunometabolic Reprogramming of human T cells

status: Public on Dec 31 2020

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: We aim to identify transciptional changes of human CD4+/CD8+ T cells due to high fat low carbohydrate ketogenic diet (KD) in vivo.
Method: Healthy volunteers conducted a 21 days ketogenic diet, limiting carbohydrate intake to <30g/day. Before the start (T0) and at the end (T1) of the diet, blood samples were taken and PBMC were isolated. PBMCs were obtained by density centrifugation (Histopaque 1077, Sigma-Aldrich, St. Louis, MO, USA). A ViCell analyzer (Beckman Coulter, Fullerton, CA, USA) was used to evaluate the cell count and viability. Only samples exceeding a cell viability of 90% were processed further. PBMCs were subjected to cell cultivation in RPMI 1640 (Invitrogen, Carlsbad, CA, USA) containing 10% heat-inactivated fetal calf serum (Biochrom, Berlin, Germany), 1% HEPES (Sigma-Aldrich, St. Louis, MO) and 1% L-glutamine (Life Technologies, Carlsbad, CA, USA). T cells were stimulated via the addition of CD3/CD28 Dynabeads (Thermo Fisher Scientific, Waltham, MA, USA) with a bead-to-cell ratio of 1:8 for a duration 24 hours.  After stimulation, CD3/CD28 Dynabeads were magnetically removed. Pan T cell-, CD4+- and CD8+-cell-isolation was performed by magnetic cell separation (Pan T Cell Isolation Kit, # 130-096-535 | human CD4 MicroBeads, # 130-045-101 | human CD8 MicroBeads, # 130-045-201, Miltenyi Biotec, Bergisch Gladbach, Germany) using an AutoMACS Pro Separator ( # 130-092-545, Miltenyi Biotec, Bergisch-Gladbach, Germany) according to the manufacturer’s instructions.
Results: 11.545 expressed genes were identified, for CD4/CD8 T cells, we detected 5.667/ 5.799 up-regulated genes and 5.878/5.746 down-regulated genes. 294/346 genes and 325/252 genes were significantly up/down-regulated for CD4+/CD8+ T cells (p-val. <0.05). Gene set enrichment analysis revealed 117/17 and 22/6 significantly up/down-regulated pathways for CD4+/CD8+ T cells (p-val. <0.05). Genes and Gene sets differentially regulated were relevant for T cell immune response and metabolic function.
Conclusion: KD resulted in immunometabolic reprogramming of human CD4+/CD8+ T cells.

overall_design: RNAseq analysis of human CD4+/CD8+ T cells prior and post 21 days of ketogenic diet

first: Gabriele

last: Strauß

first: Simon

last: Hirschberger

first: Simone

last: Kreth


title: PPARα - let-7 microRNA network in hepatic lipid metabolism [RNA-seq]

status: Public on Jan 27 2021

city: Bethesda

first: Frank

last: Gonzalez

state: Maryland

address: 9000 Rockville Pike

department: Laboratory of Metabolism

institute: National Cancer Institute

summary: Our quantitative RT-PCR analysis suggested a significant inverse relationship between PPARα activation and let-7 expression in mouse liver. Phenotypic analysis of hepatocyte-specific let-7b/c2 knockout (let7b/c2 LKO) mice showed significnat less weight gain after high-fat diet (HFD) feeding. To discover potential clues for the physiological role of let-7 miRNA in liver, RNA-seq analysis was performed in let-7b/c2 LKO mouse mice fed a HFD. Our data revealed that Let-7 miRNA disruption in hepatocytes resulted in suppression of PPARα signaling.

overall_design: Total liver RNA extracted from HFD-fed wildtype (Wildtype1, Wildtype2, Wildtype3) and let7b/c2 LKO (Let7bc2LKO1, Let7bc2LKO2, Let7bc2LKO3) mice were subjected to RNA-seq

first: Tomoki

last: Yagai


title: Conditional loss of BAF (mSWI/SNF) scaffolding subunits affects proliferation of oligodendrocyte precursors and oligodendrogenesis in developing mouse forebrain

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We report RNA-Seq from the cortex of mouse brain at P3 comparing wild types to those with conditional knockout (cKO) of BAF (mSWI/SNF) using Cre-loxP system. The Cre recombinase is expessed under GFAP promoter.

overall_design: 4 wild types vs 4 cKO

first: Kerimoglu

last: Cemil


title: Cecal microbiota transfer rescues the antibiotic-induced acceleration of type 1 diabetes and alteration of intestinal gene expression II

status: Public on Dec 28 2020

city: Piscataway

first: Xue-Song

last: Zhang

state: NJ

address: 679 Hoes Lane West, Room 113

department: CABM

institute: Rutgers University

summary: Early-life antibiotic exposure perturbs the intestinal microbiota, alters innate intestinal immunity, and accelerates type 1 diabetes development in the NOD mouse model Here we found that maternal cecal microbiota transfer (CMT) to NOD mice with early-life antibiotic perturbation partially rescued the induced T1D acceleration The restoration effects on the intestinal microbiome were substantial and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways CMT also protected against perturbed cecal and serum metabolites and normalized innate and adaptive immune effectors CMT restored patterns of ileal microRNA and histone regulation of gene expression and exon-splicing Based on the analyses of experimental data, we propose an innate intestinal immune network involving CD44, TLR2, and Reg3g, as well as their multiple microRNA and epigenetic regulators that sense intestinal signaling by the gut microbiota This regulation affects downstream immunological tone, leading to protection against the tissue-specific T1D injury

overall_design: Nanostring gene expression analysis was performed on RNA extracted from intestinal epithelial cells of male NOD mice in 3 treatments (control, antibiotic, cecal microbiota transfer) at age of P23

first: Yue

middle: S

last: Yin

first: Martin

last: Blaser


title: Global transcriptional changes upon Bromodomain (BrD) deletion in PfGCN5 and PHD domain deletion in PfPHD1 by transcriptome analyses via RNA-seq

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

summary:
Purpose: In malaria parasite, PfGCN5, a histone acetyltansferase (HAT),forms a unique complex including a PHD domain containing protein named PfPHD1. To understand the function of this complex, the BrD in PfGCN5 and PHD in PfPHD1 were deleted. The transcritional changes after domain deletions were measured by RNA-seq.
Methods: The mRNA profiles of parasite lines : 3D7 (WT), PfGCN5-ΔBrD and PfPHD1-ΔPHD, were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 in Rapid Run mode using 100nt single read sequencing. Three replicates of total RNA from parasites at ring, early trophozoite, late trophozoite and schizont stages were harvested by using the ZYMO RNA purification kit, and used to generate the sequencing libraries using the KAPA Stranded mRNA Seq kit for the Illumina sequencing platform according to the manufacturer's protocol (KAPA biosystems). Quality trimming and adapter sequence was performed using Trimmomatic (v0.36). Low quality bases were trimmed using a sliding window approach with a minimum average quality of 18 in 4 base pair window. The Reads with length <35 base pairs were removed. The trimmed reads  were mapped to the P. falciparum genome sequence (Genedb v3.1) using HISAT2 (Kim et al., 2015). The coverage was analyzed by using the bedtools (Quinlan, 2014). The expression levels and the differential expression were calculated by FeatureCounts and DESeq2 (Anders and Huber, 2010; Liao et al., 2014).
Results: Using an optimized data analysis workflow, we mapped about 5 million sequence reads per sample to the malaria parasite genome (pf3D7_V3.0.) and identified 5643 transcripts with high mapping rate at the range between 80% and 95. PfGCN5 BrD deletion profoundly disturbed the global transcription pattern, causing 3533 (62.6%) genes to be differentially expressed in at least one of the four time points analyzed. Specifically, BrD deletion resulted in down-regulation of 997, 799, 861 and 902 genes, and up-regulation of 1127, 780, 846, and 368 genes at the ring, early trophozoite, late trophozoite, and schizont stage, respectively. PHD deletion in PfPHD1 caused a similar but more profound disturbance of gene expression during the IDC, with 3870 (68.6%) transcripts being differentially expressed in at least one of the four stages analyzed. The PfPHD1 PHD deletion resulted in the down-regulation of 872, 1021, 557, and 787 genes, and up-regulation of 1481, 1266, 648, and 1028 genes at the ring, early trophozoite, late trophozoite and schizont stage, respectively.
Conclusions: Either domain deletion profoundly disturbed the global transcription pattern, causing altered expression in more than 60% of the genes including general cellular pathways such as DNA replication and translation, and parasite-specific pathways such as invasion, cytoadherence, and sexual development.

overall_design: mRNA profiles of 3D7 (WT),  PfGCN5-ΔBrD and PfPHD1-ΔPHD, were generated by deep sequencing, in triplicate

first: Jun

last: Miao

first: Liwang

last: Cui


title: Capture and identification of the eIF4E:mRNA interactome in human cells

city: Adelaide

first: Kirk

middle: B

last: Jensen

state: South Australia

address: North Terrace

department: Lifelong Health

country: Australia

institute: South Australian Health & Medical Research Institute

summary: Here we develop a novel methodology, capCLIP, to capture and identify mRNA interactions with the major cellular cap-binding protein eIF4E.

overall_design:
HeLa cells in which a 3X-flag epitope tag has been introduced on to the N-terminal end of endogenous eIF4E protein were treated with either 100 nM rapamycin (or DMSO carrier along) for 2 hours, and then subject to 350 mJ/cm2 of UV irradiation to crosslink eIF4E to the m7G cap of mRNA. Biological replicates have been done for each treatment condition.
Hela cells in which a 3X-flag epitope tag has been introduced on to the N-terminal end of endogenous eIF4E protein were serum-starved overnight then pre-treated for 1 hour with either 100 nM eFT-508 or with vehicle DMSO. Cells were then stimulated for 30 minutes with 500 nM PMA to activate MAP kinase signalling and thus MNK activity, and then subject to 350 mJ/cm2 of UV irradiation to crosslink eIF4E to the m7G cap of mRNA. Biological replicates have been done for each treatment condition.

first: John

last: Toubia


title: Single-cell transcriptomics uncovers human corneal limbal stem cells and its differentiation trajectory

status: Public on Jan 14 2021

city: Houston

first: sangbae

last: Kim

address: 1 baylor plaza

institute: Baylor College of Medicine

summary: Limbal stem cells (LSCs), known as corneal epithelial stem cells, are located at the basal epithelial layer of the corneal limbus and serve an important function in maintaining the homeostasis of the corneal epithelium.  Several putative molecular markers of LSCs have been previously identified. However, the specificity of these markers remains largely controversial. To address this gap in the current understanding of LSCs, we performed a transcriptome profiling of heterogeneous corneal limbal basal cells using single-cell transcriptomics technology to identify LSCs and their exclusive markers.  We isolated limbal basal cells from two young donors, constructed scRNA-seq libraries, generated RNA-sequencing data using the 10x Genomics platform, and then finally obtained the transcriptome of about 18,000 individual single-cells using Cell ranger (https://10xgenomics.com). Next, we performed quality control, filtering and data integration using Seurat package (https://satijalab.org/seurat), about 16,400 cells were retained for further downstream analysis such as dimensional reduction, unsupervised clustering, and Differentially expressed gene selection, trajectory analysis and visualization.  We identified 11 unique clusters of cells assigned to a putative cell type based on published known biomarkers for differentiation, proliferation and putative epithelial stem cells. As a results, we found 2 Terminally Differentiated Cell (TDC), 3 Post-Mitotic Cell (PMC), 1 Transient Amplifying Cell (TAC), 2 Limbal Progenitor Cell (LPC), Putative Limbal Stem Cell (LSC) and 2 Melanocyte (MC) sub-cell type clusters. Furthermore, we confirmed the trajectory order of LSC differentiation for 9 clusters using Pseudotemporal and Functional PCA analysis. Lastly, we validated each assigned cell subtypes and determined their location in human corneal limbus tissue with 9 markers using RNAscope   We were able to reveal the heterogeneity of corneal limbal basal epithelium by defining novel dynamic trajectories for cell types in a pseudotemporal manner. This approach allowed us to identify the distinct clusters of LSCs and progenitors with exclusively expressed markers, and might apply for translational research on regenerating a normal corneal epithelium and restoring vision.

overall_design: We isolated limbal basal cells from two young donors, constructed scRNA-seq libraries, generated RNA-sequencing data using the 10x Genomics platform, and then finally obtained the transcriptome of about 18,000 individual single-cells using Cell ranger (https://10xgenomics.com). Next, we performed quality control, filtering and data integration and further downstream analysis such as dimensional reduction, unsupervised clustering, and Differentially expressed gene selection, trajectory analysis and visualization.

first: De-Quan

last: Li

first: Jinmiao

first: Fang

last: Bian

first: Yumei

first: Rui

last: Chen


title: Quantitative transcriptome analysis of C. albicans biofilms grown in high and low carbon dioxide conditions.

status: Public on Apr 14 2021

city: Canterbury

first: Campbell

last: Gourlay

state: Kent

address: School of Biosciences, University of Kent

department: School of Biosciences

institute: University of Kent

summary: C. albicans is a dimorphic yeast which can switch from budding yeast and to hyphal forms and this property is essential for biofilm establishment and maturation. C. albicans undergoes this yeast-to-hyphal switch in response to high CO2. The purpose of this study is to use RNA-seq to investigate pathways whose genes are differentially expressed when C. albicans biofilms are grown in a physiologically relevant elevated (5%) CO2 environment compared to a low/atmospheric (0.03%) CO2 environment. We report that in C.albicans biofilms grown under 5% CO2 conditions, genes controlled by core biofilm regulatory transcription factors such as Brg1, Efg1, Ndt80, and Bcr1 are overall expressed at significantly higher levels compared to those grown in 0.03% CO2 conditions. We find that genes encoding glucose and amino acid transporters, as well as genes previously found to be involved in the response to Ketoconazole treatment, are significantly upregulated in 5% CO2 C. albicans biofilms. Overall, these data suggest a high CO2 environment enhances biofilm formation of C. albicans and may also increase antifungal tolerance of such biofilms.

overall_design: Analysis of mRNA profiles from 48hr old C. albicans (strain CAI-4) biofilms grown in 0.03% and 5% CO2 environments on silicone surfaces. RNA was extracted from 3 biological replicates for each CO2 environment.

first: Daniel

middle: R

last: Pentland

first: Jack

last: Davis

first: Friedrich

last: Mühschlegel

middle: W


title: Effect of loss of Ecdysone-induced protein 93F (E93) on the Drosophila melanogaster antennal transcriptome.

status: Public on Jan 31 2021

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Ecdysone-induced protein 93F (E93) regulates local chromatin structure and/or gene transcription, raising the question of whether expression of Ir75c, Ir75b and Ir75a receptors in antenna is affected at the transcriptional level in the absence of this protein. We performed bulk RNA-sequencing (RNA-seq) of control and E93RNAi antennae. In control RNA-seq samples, we predicted the existence of seven distinct transcripts encoded by these three receptor genes. Notably, many transcripts initiating from Ir75c do not terminate at the 3’ end of this gene but rather run through the Ir75b and Ir75a exons. Similarly, a majority of transcripts initiating from Ir75b incorporate exons 2-7 of Ir75a. The pattern of transcription is consistent with the absence of canonical transcription termination/polyadenylation sequences downstream of the Ir75c and Ir75b coding regions; such a sequence is only present 3’ of Ir75a. All transcripts initiating from Ir75c are highly up-regulated in the absence of E93, consistent with the ectopic expression of receptor protein. Transcription initiating from Ir75b is strongly diminished, concordant with the loss of Ir75b protein expression. By contrast, Ir75a transcripts levels were not significantly lower in E93RNAi antennae, despite the loss of detectable Ir75a protein.

overall_design: Three biological replicates of transgenic control and E93RNAi animals.

first: Kaan

last: Mika

first: Steeve

last: Cruchet

first: Richard

last: Benton


title: Transcriptome of Acinetobacter baumannii ATCC 17978 treated polymyxin B

status: Public on Dec 22 2020

city: Seoul

first: Jaeeun

last: Park

address: 145, Anam-ro, Seongbuk-gu, Seoul, Republic of Korea

institute: Korea university

summary: We report the trascriptomic information of wild type (Lab-WT) during the growth with or without 0.5 MIC of polymyxin B added LB (Luria-Bertani broth) media

overall_design: Examination of one Lab-WT, one Lab-WT treated 0.5 MIC of polymyxin B strain samples

first: Woojun


title: Co-existence of compulsory and plastic rRNA 2'-O-Methylation sites in human breast tumours

city: Lyon

first: Virginie

last: MARCEL

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

type: Methylation profiling by high throughput sequencing

summary: Emerging evidence suggests that changes in ribosomal RNA 2’O-ribose methylation (rRNA 2’OMe) in the human ribosome play a key role in regulating translation thereby contributing in setting particular phenotypes such as hallmarks of cancer cells. Here, by analysing the rRNA 2’OMe in a large series of 195 human primary breast tumours using the RiboMETH-seq approach  we have identified the positions within the rRNA molecules which can tolerate the absence of 2’OMe in humans. The frequency of rRNA 2’OMe at some positions is highly stable between individuals (termed “stable”) whereas it can vary substantially at other positions (termed “variant”). Differential association of rRNA 2’OMe with breast cancer features, evolution and structure/function characteristics suggest the stable positions showing a low inter-variability might be required to maintain the core structure and thus the function of the ribosome – representing compulsory rRNA 2’OMe positions. In contrast, the variant positions displaying high inter-variability might be the source of regulatory events – representing plastic rRNA 2’OMe positions. Therefore our data issued from rRNA 2’OMe profiling of a large-scale human sample series bring the first compelling evidence to resolve two divergent long lasting visions of the role of rRNA 2’O-Me and sustain the emerging role of the ribosome plasticity in regulating translation in cancer.

overall_design: rRNA 2'OMe profiling in a series of 195 primary breast tumours

last: Marcel

first: Janice

last: Kielbassa

first: Alain

last: Viari

first: Jean-Jacques

last: Diaz

first: Laurie

last: Tonon


title: Qingda granules lower Angiotensin-II-induced blood pressure

status: Public on Jan 28 2021

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

summary: The goals of this study is to compare the differently expressed genes in abdominal aorta of C57BL/6 WT mice with or without Angiotensin II (AngII) treatment as well as differently expressed genes in the abdominal aorta of WT mice with AngII treatment with or without Qingda granules (QDG) treatment. The mice (n=15) were randomly divided into 3 groups:control, AngII  and QDG treated (n=5 for each group). Mice in Control and AngII groups were infused with saline or 500 ng/kg/min of AngII respectively, and orally administrated with saline; while mice in AngII + QDG group were infused with AngII (500 ng/kg/min) and orally administrated with 1.145 g/kg /day of QDG for 2 weeks. Then the abdominal aorta were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed with abdominal aorta of  mice in 3 groups: control, AngII and QDG treated (n=5 for each group) to identify the differently expressed genes and related pathway.

first: Aling

last: Shen

first: Xiangyan

last: Wu

first: Zhiqing

first: Ying

last: Cheng


title: Retrograde labelling and RNA deep sequencing of olfactory bulb projection neurons [bulk RNA-seq]

status: Public on Dec 05 2020

city: London

first: Andreas

last: Schaefer

address: 1 Midland Road

institute: The Francis Crick Institute

summary: To characterize the molecular diversity of olfactory bulb projection neurons we used viral targeting and Fluorescence Activated Nuclei Sorting (FANS) to enrich for piriform cortex-projecting or AON-projecting neurons, and bulk RNA deep sequencing (bulk RNA deep seq) to comprehensively characterize their transcriptomes.

overall_design: To isolate GFP-labelled nuclei 6 individual replicates for each injection type were used (3 for AON and 3 for PCx-injected mice). Ipsilateral and controlateral sides were minced separately and placed into two different tubes. The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5).

first: Sara

last: Zeppilli

first: Robin

last: Attey

first: Tobias

last: Ackels

first: Stefan

last: Boeing

first: Alexander

last: Fleischmann

first: Nell

last: Klimpert

first: Anton

last: Crombach


title: Molecular diversity of olfactory bulb projection neurons

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Identification of mRNA expression patterns in the human blood thanatotranscriptome: “Dead, but not entirely”

status: Public on Dec 15 2020

city: Leuven

first: Bram

last: Bekaert

address: Herestraat 49 - box 7003 71

department: Forensic Biomedical Sciences

institute: KU Leuven

summary:
Purpose: RNA analysis of post-mortem tissues, or thanathotranscriptomics, has become a topic of interest in forensic science due to the essential information it can provide in forensic case investigations. Several studies have previously investigated the effect of death on gene transcription, but it has never been conducted with samples of the same individual.
Methods: For the first time, a longitudinal mRNA expression analysis study was performed with post-mortem human blood samples from individuals with a known time of death.
Results: The results reveal that, after death, two clearly differentiated groups of up- and down-regulated genes can be detected. Pathway analysis suggests active processes, rather than passive degradation, are the source of early post-mortem changes of gene expression in blood. In addition, a generalised linear model with an elastic net restriction predicted post-mortem interval with an RMSE of 4.88 hours.
Conclusions: Although promising, the forensic relevance of the model is currently limited and should be further improved in more extended studies.

overall_design: RNA-Seq analysis of 54 post-mortem human blood samples

first: Laura

middle: G

last: Antiga

first: Lode

last: Sibbens

first: Yasmina

last: Abbakouy

first: Ronny

last: Decorte

first: Wouter

last: Van Den Bogaert

first: Wim

last: Van de Voorde


title: QuantSeq FWD and QuantSeq REV using RNA samples from mouse NIH3T3 cells

status: Public on Jan 17 2021

first: Wei Vivian

last: Li

address: 683 Hoes Lane West

department: Biostatistics and Epidemiology

country: USA

institute: Rutgers, The State University of New Jersey

summary: Most eukaryotic genes harbor multiple cleavage and polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms. APA regulation has been implicated in a diverse array of physiological and pathological conditions. While RNA sequencing tools that generate reads containing the PAS, named onSite reads, have been instrumental in identifying PASs, they have not been widely used. By contrast, a growing number of methods generate reads that are close to the PAS, named nearSite reads, including the 3’ end counting strategy commonly used in single cell analysis. How these nearSite reads can be used for APA analysis, however, is poorly studied. Here, we present a computational method, named model-based analysis of alternative polyadenylation using 3’ end-linked reads (MAAPER), to examine APA using nearSite reads. MAAPER uses a probabilistic model to predict PASs for nearSite reads with high accuracy and sensitivity, and examines different types of APA events, including those in 3’UTRs and introns, with robust statistics. We show usability of MAAPER with data from bulk RNA and single cell samples. Our result also highlights the importance of using well annotated PASs for nearSite read analysis.

overall_design: QuantSeq FWD and QuantSeq REV libraries using RNA samples from nontreated mouse NIH3T3 cells (NT), NIH3T3 cells treated with arsenite stress for 1 hour (AS), and NIH3T3 cells that have recovered from AS treatment for 4 or 8 hours (RC4 or RC8).

first: Wei

first: Dinghai

last: Zheng

first: Ruijia

last: Wang

first: Bin

last: Tian


title: Pimary human keratinocyte knockdown with deltaNp63 specific siRNA

status: Public on Dec 08 2020

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
Human ΔNp63-specific siRNA was obtained from Invitrogen (Carlsbad, CA; sense: 5′-ACAAUGCCCAGACUCAAUU-3′; antisense: 5′-AAUUGAGUCUGGGCAUUGU-3′). Scrambled sequence siRNA for the negative control was purchased from Invitrogen. Transfections were performed using Lipofectamine RNAiMAX (Invitrogen) in Opti-MEM (GIBCO) at 40 nmol/L according to the manufacturer's instructions. The culture medium was replaced at 6 h after siRNA transfection.
mRNA was extracted from NHEKs transfected with ΔNp63-specific or scramble sequence siRNA at 72 h after transfection. Microarray slides were scanned using a 3D-GENE human 25k (TORAY, Tokyo, Japan) and microarray images were automatically analyzed with AROSTM, version 4.0 (Operon Biotechnologies, Tokyo, Japan).

overall_design: deltaNp63 knockdown keratinocyte vs control siRNA transfected keratinocyte

first: Terufumi

last: Kubo


title: DNA damage response in single RPE-FUCCI cells

status: Public on Dec 01 2020

city: Utrecht

first: Bart

last: Westendorp

address: Uppsalalaan 8

department: Molecular Health Sciences

institute: Utrecht University

summary: E2F transcription factors control the expression of a large network of cell cycle genes and are essential for S-phase entry. Cancers often demonstrate upregulation of E2F target gene expression, which can be partially explained by loss of the G1/S checkpoint and increased percentages of replicating cells. However, we now demonstrate that cycling individual neoplastic cells can display abnormally high levels of E2F-dependent transcription using single cell RNA sequencing. To test how this affects their DNA damage response, we deleted the atypical E2F transcriptional repressors (E2F7/8) in untransformed cells. This intervention specifically increased the expression of E2F target genes during S and G2-phase without overriding the G1/S-checkpoint. Live cell imaging revealed that cells in S-G2 with deregulated E2F activity failed to arrest and underwent unscheduled mitosis after neocarzinostatin-induced DNA damage. In contrast, cells with physiological E2F-activity completed S-phase and then activated the APC/C-Cdh1 via repression of the E2F-target Emi1, leading to a G1-like arrest. Interestingly, ~30% of these 4N-G1 cells could eventually inactivate APC/CCdh1 to execute a second round of DNA replication and mitosis, resulting in the formation of tetraploid cells. Cells with deregulated E2F activity fail to exit the cell cycle after DNA damage and likely acquire more genetic changes. The observed elevated E2F-dependent transcription in cancer cells could therefore potentially promote malignant progression and reduce sensitivity to anti-cancer drugs.

overall_design: Retina-pigment epithelial (RPE-hTERT) cells with stable expression of the FUCCI system were treated with 200 ng/mL neocarzinostatin or vehicle, and harvested after 24 and 48 hours. We compared E2F7/E2F8 double knockout cells with wild type cells. E2F7 and 8 were deleted using CRISPR/Cas9. Prior to single cell capturing, we either labeled E2F/8 mutant or wild type cells with the lipophilic dye DiD, and mixed the labeled and unlabeled cells prior to single cell capturing. Using fluorescence microscopy immediately prior to cell capturing and lysis we could determine the genotype of each individual cell.


title: Molecular diversity of olfactory bulb projection neurons [single-cell RNA-seq]

first: Andreas

last: Schaefer

summary:
To characterize the molecular diversity of olfactory bulb projection neurons we used viral targeting and Fluorescence Activated Nuclei Sorting (FANS) to enrich for olfactory bulb projection neurons, and single-nuclei RNA sequencing (sn-RNA seq) to comprehensively characterize their transcriptomes.
To isolate GFP-labelled nuclei, 3 individual replicates of AON and PCx-injected mice were used. Ipsilateral and controlateral sides were minced separately and placed into two different tubes. The minced tissue was gently homogenized in Nuclei PURE Lysis Buffer and 10% Triton X-100 using an ice-cold dounce and pestle, and filtered two times through a 40 μm cell strainer on ice. After centrifuging at 500 rpm for 5 min at 4 °C, the supernatant was aspirated and gently resuspended in 500 μl of cold buffer (1x of cold Hanks' Balanced Salt Solution HBSS, 1% nuclease-free BSA, RNasin Plus and 1/2000 DRAQ5).
Our study identifies molecularly distinct subtypes of mitral and tufted cells.

overall_design: we used AAV viral targeting and Fluorescence Activated Nuclei Sorting (FANS) to enrich for olfactory bulb projection neurons, and single-nuclei RNA sequencing (10x Genomics)

first: Sara

last: Zeppilli

first: Robin

last: Attey

first: Tobias

last: Ackels

first: Stefan

last: Boeing

first: Alexander

last: Fleischmann

first: Nell


title: A polycomb-independent role of EZH2 in TGFβ1-damaged epithelium triggers a fibrotic cascade with mesenchymal cells

city: Biberach

first: Karsten

last: Quast

address: Birkendorfer Str. 65

department: Computational Biology

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

summary: We sequenced mRNA from A549 and NHLFs in mono-culture and co-culture system that had been subjected to 1 ng/ml TGFß1 apically for 72h. Vehicle (HCl/BSA) treatment was used as control. 4 biological replicates for each condition.

overall_design: Transcriptional profiles of both A549 cells and NHLFs (4 donors) from mono- and co-culture were analysed with mRNA sequencing.

first: Huy

middle: Q

last: Le

first: Quast

last: Karsten